An anti-HER2 biparatopic antibody that induces unique HER2 clustering and complement-dependent cytotoxicity.

Human epidermal growth factor receptor 2 (HER2) is a receptor tyrosine kinase that plays an oncogenic role in breast, gastric and other solid tumors. However, anti-HER2 therapies are only currently approved for the treatment of breast and gastric/gastric esophageal junction cancers and treatment resistance remains a problem. Here, we engineer an anti-HER2 IgG1 bispecific, biparatopic antibody (Ab), zanidatamab, with unique and enhanced functionalities compared to both trastuzumab and the combination of trastuzumab plus pertuzumab (tras + pert). Zanidatamab binds adjacent HER2 molecules in trans and initiates distinct HER2 reorganization, as shown by polarized cell surface HER2 caps and large HER2 clusters, not observed with trastuzumab or tras + pert. Moreover, zanidatamab, but not trastuzumab nor tras + pert, elicit potent complement-dependent cytotoxicity (CDC) against high HER2-expressing tumor cells in vitro. Zanidatamab also mediates HER2 internalization and downregulation, inhibition of both cell signaling and tumor growth, antibody-dependent cellular cytotoxicity (ADCC) and phagocytosis (ADCP), and also shows superior in vivo antitumor activity compared to tras + pert in a HER2-expressing xenograft model. Collectively, we show that zanidatamab has multiple and distinct mechanisms of action derived from the structural effects of biparatopic HER2 engagement.

Method for Slater-Type Density Fitting for Intermolecular Electrostatic Interactions with Charge Overlap. I. The Model.

The effects of charge overlap, or charge penetration, are neglected in most force fields and interaction terms in QM/MM methods. The effects are however significant at intermolecular distances near the van der Waals minimum. In the present study, we propose a method to evaluate the intermolecular Coloumb interaction using Slater-type functions, thus explicitly modeling the charge overlap. The computational cost of the method is low, which allows it to be used in large systems with most force fields as well as in QM/MM schemes. The charge distribution is modeled as a distributed multipole expansion up to quadrupole and Slater-type functions of angular momentum up to L = 1. The exponents of the Slater-type functions are obtained using a divide-and-conquer method to avoid the curse of dimensionality that otherwise is present for large nonlinear optimizations. A Levenberg-Marquardt algorithm is applied in the fitting process. A set of parameters is obtained for each molecule, and the process is fully automated. Calculations have been performed in the carbon monoxide and the water dimers to illustrate the model. Results show a very good accuracy of the model with relative errors in the electrostatic potential lower than 3% over all reasonable separations. At very short distances where the charge overlaps is the most significant, errors are lower than 8% and lower than 3.5% at distances near the van der Waals minimum.

Accuracy of typical approximations in classical models of intermolecular polarization.

One of the largest limitations of standard molecular-mechanics force fields is the neglect of intermolecular polarization. Several attempts to cure this problem have been made, but the results have not always been fully satisfactory. In this paper, we present a quantitative study of the fundamental approximations that underlie polarization models for classical force fields. The induced charge density of a large set of molecular dimers is compared to supermolecular calculations for a hierarchy of simplified models. We study the effect of the Pauli principle, the local inhomogeneity of the electric field, the intramolecular coupling of the polarization response, and the fact that the induced density is a continuous function. We show that standard point-polarizability models work rather well, despite their lack of all these effects, because (1) there is a systematic error cancellation between the neglect of effects of the Pauli principle and the locally inhomogeneous electric field, and (2) the lack of intramolecular coupling and the use of a dipole expansion of the induced density have only minor effects on the polarization. However, the cancellation in (1) is not perfect, and therefore polarizable force-fields could be improved if both effects are explicitly treated.

Simulations of the absorption and fluorescence of indole in aqueous solution and at a nonpolar/polar interface.

Theoretical results are presented on the absorption and fluorescence of indole in aqueous solution as well as at the air/water surface. We use a combined quantum chemical statistical mechanical model with explicit solvent. An approximate ab initio complete active space self-consistent field description of the indole molecule is used, coupled to a discrete polarizable water medium. From the bulk simulations, strong support is found for the interchange mechanism, which explains the unusual solvent shift of the fluorescence of indole or tryptophan in a polar surrounding by a solvent induced switch of the fluorescing state. Two mechanisms are given to explain the different shifts for indole at the interface. First, a dielectric depletion effect, which is expected from the reduction of the amount of polar media. Second, an interface-specific effect, which derives from the stronger hydrogen bond formation at the surface. The latter effect acts to increase the shift for both absorption and emission at the surface as compared to the bulk. From these results, the intrinsic probe photophysics of tryptophan in proteins is discussed in terms of the properties of the protein/solvent interface and the orientation of the amino acid.

Planar or nonplanar: what is the structure of urea in aqueous solution?

A combined quantum chemical statistical mechanical method has been used to study the solvation of urea in water, with emphasis on the structure of urea. The model system consists of three parts: a Hartree-Fock quantum chemical core, 99 water molecules described with a polarizable force-field, and a dielectric continuum. A free-energy profile along the transition of urea from planar to a nonplanar structure is calculated. This mode in aqueous solution is found to be floppy. That is, the structure of urea in water is not well-defined because the planar to nonplanar transition requires an energy of the order of the thermal energy at room temperature. We discuss the implications of this finding for simulation studies of urea in polar environments like water and proteins.

p-Benzoquinone in aqueous solution: Stark shifts in spectra, asymmetry in solvent structure.

Results from a simulation of p-benzoquinone (PBQ) in water is presented. An explicit solvent representation is used together with a multiconfigurational ab initio quantum chemical method. The electronic n --> pi* transitions are studied in aqueous solution and the two such transitions are both blue-shifted but to different degree. Both non-equilibrium and many-body effects are found to have decisive influence on the solvation: despite stronger hydrogen bonding between solute and solvent in an excited state than in the ground state, there is a blue-shift, and the solvent structure around the non-polar PBQ is asymmetric, which is argued to come from special many-body effects. The unusual result of strengthened hydrogen bonds in the excited state that follows from an excitation of a non-bonding electron on a proton acceptor, is explained by the near-linear Stark shift that is present in the transition.

Many-Body Polarization, a Cause of Asymmetric Solvation of Ions and Quadrupoles.

Three models are used to study the effect of many-body polarization in the solvation of non-dipolar molecules and ions in water. Two of the models are very simplified and are used to show a number of basic principles of correlation of solvent degrees of freedom and asymmetric solvent structures. These principles are used to interpret results from the third model: an accurate simulation of para-benzoquinone (PBQ) in aqueous solution with a combined quantum chemical statistical mechanical solvent model with an explicit solvent. It is found that nonzero polarizability of PBQ introduces correlation in the solvent degrees of freedom through the many-body nature of the polarization. The fluctuating electric field from the solvent on the solute increases in magnitude with the correlation. Solvent effects are hence modified. This correlation is not described within the mean-field approximation. In practice, the correlation will show up as an increased probability for asymmetric solvation of the molecule.

pi --> n fluorescence transition in formaldehyde in aqueous solution: a combined quantum chemical statistical mechanical study.

The solvent shift to the fluorescence transition pi --> n in formaldehyde in aqueous solution is theoretically analyzed. The solvent model has explicit representation of the solvent and uses the complete active space state interaction (CASSI) method to obtain a description of the wave function of the solute similar to what the complete active space self-consistent-field (CASSCF) method would give. In the description of the solute-solvent interaction the discrete set of solvent molecules perturb the solute not only through an electrostatic perturbation but also through a nonelectrostatic operator. The latter describes in a way analogous to pseudopotential theory the effect the Pauli principle has on the solute embedded in the solvent. This way the exchange repulsion between solute and solvent is accounted for which therefore can be anisotropic. The best estimate of the average shift is a blue shift of 0.003 eV, and for the current transition the nonelectrostatic perturbation broadens the distribution but has no significant effect on the average shift.